Ted, > On another note, I know the cTAKES dictionary uses ICD9, but I'm not familiar> with how to access that information: In the example I've described below,
> where would I locate the ICD9 for a specific entity? Even though ICD9 is include in the lookup, IRRC, cTAKES by default is configured[1] only returns/stores concepts [2] that have a SNOMEDCT code or RxNorm code. [1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml [2] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java If you would like it to return ICD9 codes, one would need to modify/configure the above... --Pei On Wed, Sep 4, 2013 at 11:55 AM, Assur, Ted <theodore.as...@providence.org>wrote: > Thanks for looking into this, it's been puzzling me. > > On another note, I know the cTAKES dictionary uses ICD9, but I'm not > familiar with how to access that information: In the example I've described > below, where would I locate the ICD9 for a specific entity? > > Thank you > > Ted > > -----Original Message----- > From: Pei Chen [mailto:chen...@apache.org] > Sent: Tuesday, September 03, 2013 7:13 PM > To: dev@ctakes.apache.org > Subject: Re: specificity in selecting EntityMentions when using > AggregatePlaintextUMLSProcessor > > You're right, it should have gotten "CIN I"- that's a strange one, > probably needs to be debugged/looked into further... > > On Tue, Sep 3, 2013 at 10:05 PM, Miller, Timothy < > timothy.mil...@childrens.harvard.edu> wrote: > > Ah. So it will get > > CIN 2 (in SNOMED) > > CIN III (in SNOMED) > > CIN 3 (in SNOMED) > > > > but the rest are not in SNOMED? > > > > I wonder why it doesn't get CIN I? It looks like that exists in SNOMED > > (though I don't fully understand what all the symbols mean in the umls > > browser). > > > >> CIN I - Cervical intraepithelial neoplasia 1 > >> [A3002690/SNOMEDCT/SY/285836003] > > > > > > On 09/03/2013 09:55 PM, Pei Chen wrote: > >> It has the correct parse (POS, chunks, and lookupwindow)- but some of > >> the terms do not exist in SNOMED- CIN 2 - Cervical intraepithelial > >> neoplasia 2 [A3002688/SNOMEDCT/SY/285838002] exists but not CIN II. > >> CIN III [A3333965/SNOMEDCT/SY/20365006] also exists that's why it was > >> able to perform the lookup successfully. > >> Note that CIN II synonyms do exist in other umls thersauses such as > >> MEDCIN, CCPSS though. However, the bundled cTAKES dictionaries only > >> contain (MeSH, SNOMEDCT, RxNORM, NCI, ICD9) IRRC. > >> > >> --Pei > >> > >> On Tue, Sep 3, 2013 at 9:44 PM, Miller, Timothy > >> <timothy.mil...@childrens.harvard.edu> wrote: > >>> That is a good question, Ted! > >>> > >>> I tried it with a simple context: "The patient has a CIN III." I'm > >>> not sure if that is a correct context but I was able to duplicate > >>> your findings. (Finds a CUI for CIN III but not if you change it to > >>> CIN II) > >>> > >>> My first thought was that it is the chunker. But the chunker seems > >>> to get it right, as CIN II and CIN III are both called NPs, and > >>> similarly the LookupWindowAnnotator handles them both identically. > >>> So that suggests it is a problem with the actual lookup of the > >>> tokens in the LookupWindow. > >>> > >>> That's all I can do for now but maybe someone else who knows more > >>> about its behavior offhand will have an idea. > >>> > >>> Tim > >>> > >>> > >>> > >>> > >>> On 09/03/2013 08:24 PM, Assur, Ted wrote: > >>>> I'm trying to understand what would prevent the > AggregatePlaintextUMLSProcessor AE from correctly parsing specific problems > that are defined in the UMLS version used by cTAKES. > >>>> > >>>> For example, > >>>> CIN (Cervical Intraepithelial Neoplasia) in its general usage is > parsed out as UMLS CUI C0206708. > >>>> > >>>> CIN comes in 3 grades, 1, 2 and 3. Sometimes this is reported with > Roman Numerals, I,II, and III. > >>>> > >>>> cTAKES correctly identifies "CIN 3" and "CIN III" with UMLS CUI > C0851140: "Carcinoma in situ of uterine cervix." > >>>> > >>>> However, I cannot get it to recognize CIN 1, CIN I, CIN 2, or CIN II > as their correct concepts, "Cervical intraepithelial neoplasia grade 1" and > "Cervical intraepithelial neoplasia grade 2" respectively. > >>>> > >>>> Is there a way to tune the detection of UMLS concepts? > >>>> > >>>> > >>>> > >>>> > >>>> -------------------------------------------- > >>>> Ted Assur > >>>> IT Solutions Architect for Cancer Research Providence Health & > >>>> Services ted.as...@providence.org > >>>> 503-215-6476 > >>>> > >>>> Crede, ut intelligas. > >>>> Intellego, ut credam. > >>>> > >>>> > >>>> > >>>> > >>>> ________________________________ > >>>> > >>>> This message is intended for the sole use of the addressee, and may > contain information that is privileged, confidential and exempt from > disclosure under applicable law. If you are not the addressee you are > hereby notified that you may not use, copy, disclose, or distribute to > anyone the message or any information contained in the message. If you have > received this message in error, please immediately advise the sender by > reply email and delete this message. > >>>> > > > > > ________________________________ > > This message is intended for the sole use of the addressee, and may > contain information that is privileged, confidential and exempt from > disclosure under applicable law. If you are not the addressee you are > hereby notified that you may not use, copy, disclose, or distribute to > anyone the message or any information contained in the message. If you have > received this message in error, please immediately advise the sender by > reply email and delete this message. > >
